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Python
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import os.path import sys import hashlib import pytest import numpy as np from numpy.exceptions import AxisError from numpy.linalg import LinAlgError from numpy.testing import ( assert_, assert_raises, assert_equal, assert_allclose, assert_warns, assert_no_warnings, assert_array_equal, assert_array_almost...
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Python
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import warnings warnings.simplefilter("ignore") import os os.environ["KIVY_NO_CONSOLELOG"] = "1" from numpy.core.numeric import ones from pandas._config.config import set_option from kivy.app import App from kivy.uix.floatlayout import FloatLayout from kivy.factory import Factory from kivy.properties import ObjectPro...
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Python
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""" test label based indexing with loc """ from collections import namedtuple from datetime import ( date, datetime, time, timedelta, ) import re from dateutil.tz import gettz import numpy as np import pytest from pandas._config import using_pyarrow_string_dtype from pandas._libs import index as libi...
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Python
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import datetime import numpy as np import pytest import pytz import pandas.util._test_decorators as td import pandas as pd from pandas import ( Index, Timedelta, merge_asof, option_context, to_datetime, ) import pandas._testing as tm from pandas.core.reshape.merge import MergeError @pytest.fixt...
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Python
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import datetime import pickle import pytest import numpy import numpy as np from numpy.testing import ( IS_WASM, assert_, assert_equal, assert_raises, assert_warns, suppress_warnings, assert_raises_regex, assert_array_equal, ) # Use pytz to test out various time zones if available try: from pytz ...
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Python
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import numpy as np import time import graph_tool as gt from graph_tool import draw as gdraw from graph_tool import topology as gtop import lcapy import PySpice.Logging.Logging as Logging logger = Logging.setup_logging() from PySpice.Spice.Netlist import Circuit from PySpice.Unit import * class pipenet(): ''' Class...
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Python
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#!/usr/bin/env python3 # Tests implemented in this file are relying on GitHub GraphQL APIs # In order to avoid test flakiness, results of the queries # are cached in gql_mocks.json # PyTorch Lint workflow does not have GITHUB_TOKEN defined to avoid # flakiness, so if you are making changes to merge_rules or # GraphQL ...
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Python
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import array from collections import ( OrderedDict, abc, defaultdict, namedtuple, ) from collections.abc import Iterator from dataclasses import make_dataclass from datetime import ( date, datetime, timedelta, ) import functools import re import numpy as np from numpy import ma from numpy.m...
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Python
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# TODO: Add Generic type annotations to initialized collections. # For now we'd simply use implicit Any/Unknown which would add redundant annotations # mypy: disable-error-code="var-annotated" """ Package resource API -------------------- A resource is a logical file contained within a package, or a logical subdirecto...
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Python
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""" This modules specifies contrasts for the IBC tasks Author: Bertrand Thirion, Ana Luisa Pinho 2014--2020 """ import numpy as np def make_contrasts(paradigm_id, design_matrix_columns=None): """ return the contrasts matching a string""" if paradigm_id == 'ArchiStandard': return archi_standard(desig...
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Python
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#!/usr/bin/env python3 from __future__ import annotations import base64 import json import os import re import time import traceback import urllib.parse from collections import defaultdict from dataclasses import dataclass from functools import cache, partial from pathlib import Path from re import Pattern from typin...
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Python
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import sys import pytest import textwrap import subprocess import numpy as np import numpy._core.umath as ncu import numpy._core._multiarray_tests as _multiarray_tests from numpy import array, arange, nditer, all from numpy.testing import ( assert_, assert_equal, assert_array_equal, assert_raises, IS_WASM, HA...
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Python
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import warnings import itertools import sys import ctypes as ct import pickle import pytest from pytest import param import numpy as np import numpy._core.umath as ncu import numpy._core._umath_tests as umt import numpy.linalg._umath_linalg as uml import numpy._core._operand_flag_tests as opflag_tests import numpy._c...
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Python
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import copy import os import torch import networkx as nx from utils import one_hot from rules import ( ATOMIC_NUMBER, CHARGE_CATEGORIES, HYBRIDIZATION_CATEGORIES, FRAGMENTS, MAX_VALENCE, bond_orders, node_valence_degree, atomic_num_at, atomic_charge_at, adjacency...
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Python
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from __future__ import annotations import os import time from pathlib import Path from typing import TYPE_CHECKING, Any, cast import numpy as np import tifffile import useq from ndv import NDViewer from pymmcore_widgets.useq_widgets._well_plate_widget import ( DATA_POSITION, WellPlateView, ) from qtpy.QtCore ...
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Python
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""" Module contains tools for processing Stata files into DataFrames The StataReader below was originally written by Joe Presbrey as part of PyDTA. It has been extended and improved by Skipper Seabold from the Statsmodels project who also developed the StataWriter and was finally added to pandas in a once again improv...
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""" Created on Jan 8, 2026 Classify modulation of corticospinal excitability (MEP) using p-values of t-tests. Only run one model for experiment 1A. For publication. Has main function. @author: mning STATUS: WIP. FOR PUBLICATION: Unknown. SYNTAX: Script. DESCRIPTION: Performs classification of entropies. ...
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#!/usr/bin/env python3 """ Scientific workflow ------------------- * Recursively inventory EEG-Pype .txt output. * Keep sensor-level and each source method / atlas / region selection separate. * Prefer unfiltered data and otherwise use the widest passband that covers the fit. * Calculate a multitaper PSD for each saved...
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EMOJI = { "1st_place_medal": "🥇", "2nd_place_medal": "🥈", "3rd_place_medal": "🥉", "ab_button_(blood_type)": "🆎", "atm_sign": "🏧", "a_button_(blood_type)": "🅰", "afghanistan": "🇦🇫", "albania": "🇦🇱", "algeria": "🇩🇿", "american_samoa": "🇦🇸", "andorra": "🇦🇩", ...
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from __future__ import annotations from collections.abc import ( Collection, Generator, Hashable, Iterable, Sequence, ) from functools import wraps from sys import getsizeof from typing import ( TYPE_CHECKING, Any, Callable, Literal, cast, ) import warnings import numpy as np ...
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Python
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"""Module containing non-deprecated functions borrowed from Numeric. """ import functools import types import warnings import numpy as np from .._utils import set_module from . import multiarray as mu from . import overrides from . import umath as um from . import numerictypes as nt from .multiarray import asarray, a...
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Python
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from __future__ import annotations import contextlib from contextlib import closing import csv from datetime import ( date, datetime, time, timedelta, ) from io import StringIO from pathlib import Path import sqlite3 from typing import TYPE_CHECKING import uuid import numpy as np import pytest from p...
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Python
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## ........................................................................... ## ## PIMMS (Polymer Interactions in Multicomponent Mixtures) ## Alex Holehouse, Pappu Lab, Holehouse Lab ## Copyright 2015 - 2026 ## ........................................................................... ## ## simulation ## ## This f...
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""" Quantum state and operator class backend by tensornetwork """ # pylint: disable=invalid-name import logging import math import os import warnings from functools import partial, reduce from operator import matmul, mul, or_ from collections import Counter from typing import ( Any, Callable, Collection, ...
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""" Created on Jan 5, 2026 Run regression on TEP ratios using entropy as predictors. @author: mning STATUS: WIP. FOR PUBLICATION: Unknown. SYNTAX: Script. DESCRIPTION: Performs classification of entropies. Look at second feature set. PIPELINE SUMMARY: RESTRICTION: 1) Feature selection option is not p...
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Python
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""" crackfortran --- read fortran (77,90) code and extract declaration information. Copyright 1999 -- 2011 Pearu Peterson all rights reserved. Copyright 2011 -- present NumPy Developers. Permission to use, modify, and distribute this software is given under the terms of the NumPy License. NO WARRANTY IS EXPRESSED OR ...
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Python
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""" Simulation code for the Amygdala Engrams model. At the bottom of this file, you will find the main method. Please simply uncomment the line for the figure which you would like to reproduce. """ from model.phase import Phase from model.model import AmygdalaEngrams import numpy as np import matplotlib.pyplot as pl...
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Python
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import marimo __generated_with = "0.18.0" app = marimo.App(width="medium", auto_download=["ipynb"]) @app.cell def _(): import os from datetime import datetime import numpy as np import pandas as pd import scipy.stats as stats import statsmodels.formula.api as smf # Local module imports ...
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Python
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""" Module for applying conditional formatting to DataFrames and Series. """ from __future__ import annotations from contextlib import contextmanager import copy from functools import partial import operator from typing import ( TYPE_CHECKING, Any, Callable, overload, ) import warnings import numpy as...
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Python
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import sys import warnings import itertools import platform import pytest import math from decimal import Decimal import numpy as np from numpy._core import umath, sctypes from numpy._core.numerictypes import obj2sctype from numpy.exceptions import AxisError from numpy.random import rand, randint, randn from numpy.tes...
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Python
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#!/usr/bin/env python # -*- coding: utf-8 -*- """ This experiment was created using PsychoPy3 Experiment Builder (v2023.2.3), on June 19, 2024, at 12:46 If you publish work using this script the most relevant publication is: Peirce J, Gray JR, Simpson S, MacAskill M, Höchenberger R, Sogo H, Kastman E, L...
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"""Tests for the CaliRunner and internal runners. Optimized for CI speed while maintaining >90% coverage. Key optimizations: 1. Mock cellpose inference in most tests (cellpose is slow) 2. Use fixtures to share database setup where possible """ import gc from collections.abc import Generator, Iterator from pathlib imp...
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Python
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## ........................................................................... ## ## PIMMS (Polymer Interactions in Multicomponent Mixtures) ## Alex Holehouse, Pappu Lab, Holehouse Lab ## Copyright 2015 - 2026 ## ........................................................................... import random import math im...
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Python
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import torch from torch.optim import Adam import torch.nn.functional as F from gym.spaces import Box, Discrete, MultiDiscrete from multiagent.multi_discrete import MultiDiscrete from utils.networks import MLPNetwork, SNNNetwork from utils.misc import soft_update, average_gradients, onehot_from_logits, gumbel_softmax fr...
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import marimo __generated_with = "0.18.2" app = marimo.App(width="medium", auto_download=["ipynb"]) @app.cell def _(): import os from datetime import datetime import numpy as np import pandas as pd import scipy.stats as stats import statsmodels.formula.api as smf # Local module imports ...
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import marimo __generated_with = "0.18.2" app = marimo.App(width="medium", auto_download=["ipynb"]) @app.cell def _(): import os from datetime import datetime import numpy as np import pandas as pd import scipy.stats as stats import statsmodels.formula.api as smf # Local module imports ...
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"""@authors: Herman van Dellen en Yorben Lodema.""" import itertools import json import logging import math import os import pickle import random import re import time from collections import defaultdict from datetime import datetime from multiprocessing import Pool, cpu_count from typing import Optional import mne i...
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import operator import warnings import sys import decimal from fractions import Fraction import math import pytest import hypothesis from hypothesis.extra.numpy import arrays import hypothesis.strategies as st from functools import partial import numpy as np from numpy import ( ma, angle, average, bartlett, blackm...
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""" Created on Dec 19, 2024 Classify plasticity in corticospinal excitability (MEP). @author: mning """ """ STATUS: WIP. FOR PUBLICATION: Unknown. SYNTAX: Script. DESCRIPTION: Performs classification of entropies. Look at second feature set. PIPELINE SUMMARY: RESTRICTION: 1) Feature selection option i...
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Python
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import marimo __generated_with = "0.18.0" app = marimo.App(width="medium", auto_download=["ipynb"]) @app.cell def _(): import os import re from pathlib import Path from datetime import datetime import numpy as np import pandas as pd import scipy.stats as stats import statsmodels.formu...
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""" NO LONGER IN USE, use calc_Classification_Entropy_Ratio_2.py Created on Dec 23, 2024 @author: mning STATUS: WIP. FOR PUBLICATION: Unknown. SYNTAX: Script. DESCRIPTION: Performs classification of powers of different frequency bands and plot different performance metrics. Additional debugging informat...
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Python
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""" Created on Apr 28, 2025 To compare two files, use git diff: git diff --no-index calc_Classification_Entropy_Ratio_02.py calc_Classification_Entropy_Ratio_2.py Diff between calc_Classification_Entropy_Ratio.py: Use entropy from rf"Entropy_{band_name}_{inpt_op_str}_02_Full.csv" instead of rf"Entropy_{band_name}_{i...
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Python
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""" High level interface to PyTables for reading and writing pandas data structures to disk """ from __future__ import annotations from contextlib import suppress import copy from datetime import ( date, tzinfo, ) import itertools import os import re from textwrap import dedent from typing import ( TYPE_CH...
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""" Simulation code for the Amygdala Engrams model. At the bottom of this file, you will find the main method. Please simply uncomment the line for the figure which you would like to reproduce. """ from model.phase import Phase from model.model import AmygdalaEngrams import numpy as np import matplotlib.pyplot as pl...
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Python
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""" UNTESTED Created on Apr 9, 2025 To compare two files, use git diff: git diff --no-index calc_Classification_Entropy_Ratio_02.py calc_Classification_Entropy_Ratio_2.py Diff between calc_Classification_Entropy_Ratio.py: Use entropy from rf"Entropy_{band_name}_{inpt_op_str}_02_Full.csv" instead of rf"Entropy_{band...
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Python
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""" Created on Oct 21, 2024 To compare two files, use git diff: git diff --no-index calc_Classification_Entropy_Ratio_02.py calc_Classification_Entropy_Ratio_2.py Diff between calc_Classification_Entropy_Ratio.py: Use entropy from rf"Entropy_{band_name}_{inpt_op_str}_02_Full.csv" instead of rf"Entropy_{band_name}_{i...
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Python
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""" Created on Apr 9, 2025 To compare two files, use git diff: git diff --no-index calc_Classification_Entropy_Ratio_02.py calc_Classification_Entropy_Ratio_2.py Diff between calc_Classification_Entropy_Ratio.py: Use entropy from rf"Entropy_{band_name}_{inpt_op_str}_02_Full.csv" instead of rf"Entropy_{band_name}_{in...
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Python
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import platform import warnings import fnmatch import itertools import pytest import sys import operator from fractions import Fraction from functools import reduce from collections import namedtuple import numpy._core.umath as ncu from numpy._core import _umath_tests as ncu_tests, sctypes import numpy as np from nump...
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Python
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""" Provide the groupby split-apply-combine paradigm. Define the GroupBy class providing the base-class of operations. The SeriesGroupBy and DataFrameGroupBy sub-class (defined in pandas.core.groupby.generic) expose these user-facing objects to provide specific functionality. """ from __future__ import annotations fr...
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Python
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import builtins import collections.abc import functools import re import sys import warnings import numpy as np import numpy._core.numeric as _nx from numpy._core import transpose, overrides from numpy._core.numeric import ( ones, zeros_like, arange, concatenate, array, asarray, asanyarray, empty, ndarray, tak...
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Python
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"""@authors: Herman van Dellen and Yorben Lodema.""" import os import json import pickle import posixpath import traceback import webbrowser as wb from datetime import datetime from pathlib import Path import gc import mne import mne_icalabel import numpy as np import pandas as pd from mne.beamformer import apply_lcm...
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# module pyparsing.py # # Copyright (c) 2003-2018 Paul T. McGuire # # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files (the # "Software"), to deal in the Software without restriction, including # without limitation the rights to use, cop...
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""" This is only meant to add docs to objects defined in C-extension modules. The purpose is to allow easier editing of the docstrings without requiring a re-compile. NOTE: Many of the methods of ndarray have corresponding functions. If you update these docstrings, please keep also the ones in _core/fromnu...
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Python
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# pylint: disable-msg=W0400,W0511,W0611,W0612,W0614,R0201,E1102 """Tests suite for MaskedArray & subclassing. :author: Pierre Gerard-Marchant :contact: pierregm_at_uga_dot_edu """ __author__ = "Pierre GF Gerard-Marchant" import sys import warnings import copy import operator import itertools import textwrap import pi...
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""" DataFrame --------- An efficient 2D container for potentially mixed-type time series or other labeled data series. Similar to its R counterpart, data.frame, except providing automatic data alignment and a host of useful data manipulation methods having to do with the labeling information """ from __future__ import...
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""" numpy.ma : a package to handle missing or invalid values. This package was initially written for numarray by Paul F. Dubois at Lawrence Livermore National Laboratory. In 2006, the package was completely rewritten by Pierre Gerard-Marchant (University of Georgia) to make the MaskedArray class a subclass of ndarray,...
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Python
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from __future__ import annotations import collections.abc import tempfile import sys import warnings import operator import io import itertools import functools import ctypes import os import gc import re import weakref import pytest from contextlib import contextmanager import pickle import pathlib import builtins fr...
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# pyright: reportPropertyTypeMismatch=false from __future__ import annotations import collections from copy import deepcopy import datetime as dt from functools import partial import gc from json import loads import operator import pickle import re import sys from typing import ( TYPE_CHECKING, Any, Callab...
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from __future__ import annotations from collections import abc from datetime import datetime import functools from itertools import zip_longest import operator from typing import ( TYPE_CHECKING, Any, Callable, ClassVar, Literal, NoReturn, cast, final, overload, ) import warnings i...
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""" Data structure for 1-dimensional cross-sectional and time series data """ from __future__ import annotations from collections.abc import ( Hashable, Iterable, Mapping, Sequence, ) import operator import sys from textwrap import dedent from typing import ( IO, TYPE_CHECKING, Any, Cal...
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# This file is automatically generated by tools/idna-data # vim: set fileencoding=utf-8 : from typing import List, Tuple, Union """IDNA Mapping Table from UTS46.""" __version__ = "15.1.0" def _seg_0() -> List[Union[Tuple[int, str], Tuple[int, str, str]]]: return [ (0x0, "3"), (0x1, "3"), ...
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Quarto
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--- title: "maxSPRT: maximise the spirit of pharmacovigilance" author: "{...} from QUMPRC @UniSA" format: revealjs --- ## Outline 1. The problem + The data + Primer/example of multiple comparison problem 2. Solutions + Some terminology 3. Comparison of solutions: RR vs LLR + The idea behind RR to find...
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--- title: "import_trial_times" format: html: self-contained: true code-tools: true --- ```{r} #| label: setup #| include: false library(tidyverse) library(readxl) library(melidosData) source("../project_globals.R") ``` ```{r} path_study_dates <- paste0("../data/Study_dates_MeLiDos_", site, ".xlsx") #imp...
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Quarto
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--- title: "Consistency of maxSPRT critical value calculations across packages in R" subtitle: "Signal detection of spontaneous medical device reports over time accounting for multiple comparisons" author: "Ty Stanford et al." format: pdf: toc: true highlight-style: atom-one number-sections: true editor:...
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Quarto
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--- title: "Data preprocessing for analysis" subtitle: "Signal detection of spontaneous medical device reports over time" author: "Ty Stanford and Curtis Murray" format: pdf: toc: true highlight-style: atom-one number-sections: true editor: source --- <!-- highlight-style supported themes: arrow, pygme...
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Quarto
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--- title: "Data analysis" subtitle: "Signal detection of spontaneous medical device reports over time" author: "Ty Stanford et al." format: pdf: toc: true highlight-style: atom-one number-sections: true editor: source --- <!-- highlight-style supported themes: arrow, pygments, tango, espresso, zenburn...
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Quarto
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--- title: "Import demographics" author: "Johannes Zauner" format: html: self-contained: true code-tools: true editor_options: chunk_output_type: console --- ## Preface This document imports the `demographics` and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tid...
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Quarto
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--- title: "Import lifestyle and health" author: "Johannes Zauner" format: html: self-contained: true code-tools: true editor_options: chunk_output_type: console --- ## Preface This document imports the `health` questionnaire and shows descriptive statistics for the site. ## Setup ```{r} #| message: f...
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Quarto
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--- title: "Import Light sensitivity VLSQ8" author: "Johannes Zauner" format: html: self-contained: true code-tools: true editor_options: chunk_output_type: console --- ## Preface This document imports the `VLSQ8` (Light sensitivity) and shows descriptive statistics for the site. ## Setup ```{r} #| me...
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Quarto
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--- title: "Import light glasses acceptability" author: "Johannes Zauner" format: html: self-contained: true code-tools: true editor_options: chunk_output_type: console --- ## Preface This document imports the `acceptability` (of light glasses) and shows descriptive statistics for the site. ## Setup `...
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Quarto
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--- title: "Import wellbeing diary" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- ## Preface This document imports the `WHO5` wellbeing diary and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyverse) library(LightLogR) library(...
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Quarto
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--- title: "Import current conditions" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- ## Preface This document imports the `current conditions` and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyverse) library(LightLogR) library...
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--- title: "Import Sleep environment ASE" author: "Johannes Zauner" format: html: self-contained: true code-tools: true editor_options: chunk_output_type: console --- ## Preface This document imports the `ASE` (Sleep environment) and shows descriptive statistics for the site. ## Setup ```{r} #| messag...
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--- title: "Import LEBA" author: "Johannes Zauner" format: html: self-contained: true code-tools: true editor_options: chunk_output_type: console --- ## Preface This document imports the `LEBA` and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyverse) library(...
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--- title: "Import light wrist" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- # Preface This is a work-in-progress descriptive analysis of the `SanchoSalasEtAl2025` dataset. ```{r} #| label: setup #| include: false library(LightLogR) library(glue) library(tidyverse) lib...
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--- title: "Import light glasses" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- # Preface This is a work-in-progress descriptive analysis of the `SanchoSalasEtAl2025` dataset. ```{r} #| label: setup #| include: false library(LightLogR) library(glue) library(tidyverse) l...
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--- title: "Import light chest" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- # Preface This is a work-in-progress descriptive analysis of the `SanchoSalasEtAl2025` dataset. ```{r} #| label: setup #| include: false library(LightLogR) library(glue) library(tidyverse) lib...
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--- title: "Import exercise diaries" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- ## Preface This document imports the `exercisediary` and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyverse) library(LightLogR) library(glue) ...
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--- title: "Import sleep diaries" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- ## Preface This document imports the `sleepdiaries` and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyverse) library(LightLogR) library(glue) libr...
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--- title: "Import light glasses evaluation" author: "Johannes Zauner" format: html: self-contained: true code-tools: true editor_options: chunk_output_type: console --- ## Preface This document imports the `evaluation` (of using light glasses/and lanyrads) and shows descriptive statistics for the site....
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--- title: "Import experience log" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- ## Preface This document imports the `experience log` and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyverse) library(LightLogR) library(glue) l...
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Quarto
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--- title: "Import wearlog" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- ## Preface This document imports the `wear log` and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyverse) library(LightLogR) library(glue) library(readxl...
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--- title: "Import chronotype" author: "Johannes Zauner" format: html: self-contained: true code-tools: true editor_options: chunk_output_type: console --- ## Preface This document imports the `chronotype` and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyver...
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Quarto
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--- title: "Import mHLEA" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- ## Preface This document imports the `mHLEA` evening diary (light exposure) and shows descriptive statistics for the site. ## Setup ```{r} #| message: false library(tidyverse) library(LightLogR) li...
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--- title: "Descriptive analysis" author: "Johannes Zauner" format: html: self-contained: true code-tools: true --- # Preface This is a work-in-progress descriptive analysis of the `Sancho-SalasEtAl2025` dataset. ```{r} #| label: setup #| include: false library(LightLogR) library(glue) library(tidyverse) ...
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--- title: "" format: docx: reference-doc: landscape-template.docx --- ## sumary of events in table (no Description field) | Report_ID | Report date | Classification | Device | P('pain'\|doc) | Event | Event type | Source | |--------:|:--------|:--------|:--------|------...
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--- title: "Report" subtitle: "Signal detection of spontaneous medical device reports over time accounting for multiple comparisons" author: "Ty Stanford, Lan Kelly, Marianne Gillam, et al." format: docx: toc: true highlight-style: atom-one number-sections: true pdf: toc: true highlight-style: ...
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--- title: "ASO F. Prausnitzii Treatment Bulk RNA-Seq Analysis" editor: source author: "Joe Boktor" date: '2025-05-04' format: html: self-contained: true code-fold: false code-tools: true fig-align: center fig-height: 12 fig-width: 18 toc: true toc-location: left toc-title: "Conte...
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--- title: "Figures" author: "T. Macedo" format: html --- This quarto document is a script to reproduce figures using the data and modeling in the methods of "Growth for coral reefs peaked at 25 °C through the Holocene" in PLOS ONE by Tonya Macedo and Robert van Woesik ----------------------------- Figure...
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R
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site <- "UCR"
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R
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".RNG.name" <- "base::Mersenne-Twister" ".RNG.seed" <- 1
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R
57
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".RNG.name" <- "base::Mersenne-Twister" ".RNG.seed" <- 3
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R
57
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".RNG.name" <- "base::Mersenne-Twister" ".RNG.seed" <- 2
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R
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library(shiny) ui <- source('ui.R') server <- source('server.R') shinyApp(ui, server)
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R
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library(testthat) library(miloR) require(mvtnorm) require(scran) require(scater) require(MASS) test_check("miloR")
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R
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library(cowplot) plot_grid(spontaneous_rotarod, mptp_rotarod_plot,pff_data_positive_plot, aso_data_positive_plot,nrow=1)
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R
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# this script is run before any of the test_*.R scripts # include this code before unit testing @ https://github.com/r-lib/testthat/issues/544 source("../prepare_test_datasets.R")
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R
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8
# Wrapper for `scale()` in cases where sd(x) == 0 scale2 <- function(x) { if (near(sd(x), 0)) { scale(x, center = TRUE, scale = FALSE) } else { scale(x, center = TRUE, scale = TRUE) } }
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R
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save_pheatmap_pdf <- function(x, filename, width=7, height=7) { stopifnot(!missing(x)) stopifnot(!missing(filename)) pdf(filename, width=width, height=height) grid::grid.newpage() grid::grid.draw(x$gtable) dev.off() }
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R
242
12
library(readr) library(lme4) library(lmerTest) library(emmeans) df <- read_csv("collected_results.csv") df$jitter <- factor(df$jitter) m1 <- lmer("perc_correct ~ jitter + (1|pid)", data = df) anova(m1) em <- emmeans(m1, 'jitter') pairs(em)